# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 19:32:55 2020
#   Inital geometry file: a 48 line input string
#   Ligand name: (4R)-4-hydroxy-2,5-dioxopentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H](CC(=O)C(O)=O)C=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 GXS  GXS  '(4R)-4-hydroxy-2,5-dioxopentanoic acid'  ligand  15  10  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GXS
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 GXS  O   O  O      0  -0.374  -3.6635   0.7436   0.2718
 GXS  C   C  C1     0   0.157  -2.7136   0.6717  -0.4649
 GXS  C1  C  CH1    0  -0.065  -1.5732  -0.2966  -0.2876
 GXS  O1  O  OH1    0  -0.652  -1.7964  -1.2142   0.7408
 GXS  C2  C  CH2    0  -0.598  -0.2864   0.5065  -0.1150
 GXS  C3  C  C      0   0.248   0.9657  -0.3261  -0.2490
 GXS  C4  C  C      0   0.352   2.3122   0.3612   0.1295
 GXS  O3  O  OC    -1  -0.579   3.3319  -0.2985  -0.1080
 GXS  O4  O  O      0  -0.575   2.2096   1.4960   0.6242
 GXS  H1  H  H      0   0.196  -2.6071   1.3398  -1.3377
 GXS  H2  H  HCH1   0   0.269  -1.5093  -0.8660  -1.2234
 GXS  H3  H  HOH1   0   0.446  -2.0046  -0.7303   1.5475
 GXS  H4  H  HCH2   0   0.281  -0.2225   1.3034  -0.8657
 GXS  O2  O  O      0  -0.387   0.9397  -1.4616  -0.6563
 GXS  H8  H  HCH2   0   0.281  -0.2821   1.0260   0.8469

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 GXS  O1  C1  single  1.396  0.020  1.396
 GXS  C3  C2  single  1.510  0.020  1.510
 GXS  C3  C4  single  1.558  0.020  1.558
 GXS  C2  C1  single  1.527  0.020  1.527
 GXS  O4  C4  deloc   1.242  0.020  1.242
 GXS  C1  C   single  1.506  0.020  1.506
 GXS  C4  O3  deloc   1.238  0.020  1.238
 GXS  C   O   double  1.204  0.020  1.204
 GXS  C   H1  single  0.930  0.020  1.080
 GXS  C1  H2  single  0.970  0.020  1.090
 GXS  O1  H3  single  0.850  0.020  0.980
 GXS  C2  H4  single  0.970  0.020  1.090
 GXS  C3  O2  double  1.207  0.020  1.207
 GXS  C2  H8  single  0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 GXS  H1  C   C1  114.14  3.000
 GXS  H1  C   O   121.56  3.000
 GXS  C1  C   O   124.29  3.000
 GXS  H2  C1  C2  108.68  3.000
 GXS  H2  C1  O1  107.25  3.000
 GXS  C2  C1  O1  113.40  3.000
 GXS  H2  C1  C   106.10  3.000
 GXS  C2  C1  C   108.25  3.000
 GXS  O1  C1  C   112.84  3.000
 GXS  H3  O1  C1  108.73  3.000
 GXS  H8  C2  H4  104.88  3.000
 GXS  H8  C2  C3  109.69  3.000
 GXS  H4  C2  C3  106.96  3.000
 GXS  H8  C2  C1  110.66  3.000
 GXS  H4  C2  C1  110.73  3.000
 GXS  C3  C2  C1  113.51  3.000
 GXS  O2  C3  C4  121.03  3.000
 GXS  O2  C3  C2  122.08  3.000
 GXS  C4  C3  C2  116.86  3.000
 GXS  O4  C4  O3  129.16  3.000
 GXS  O3  C4  C3  115.49  3.000
 GXS  O4  C4  C3  115.36  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 GXS  Var_01  C4  C3  C2  C1  -170.79  30.0  1
 GXS  Var_02  O4  C4  C3  C2     6.35  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 GXS  chir_01  C1  O1  C2  C  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 GXS  plan-1  C2  0.020
 GXS  plan-1  C3  0.020
 GXS  plan-1  C4  0.020
 GXS  plan-1  O2  0.020
 GXS  plan-2  C3  0.020
 GXS  plan-2  C4  0.020
 GXS  plan-2  O3  0.020
 GXS  plan-2  O4  0.020
 GXS  plan-3  O   0.020
 GXS  plan-3  C   0.020
 GXS  plan-3  C1  0.020
 GXS  plan-3  H1  0.020

